The rational was that the output also includes a PDF folder. However this can be confusing as putting the path in output_vcf is tempting. I propose to change the behaviour as follow:
--output_vcf: is the path to the output vcf (e.g. my_vcf.vcf or /path/to/my_vcf.vf or ../my_vcf.vcf)
--output_pdf: is optional and is the folder where to store the PDF folder (e.g. . or /path/to/outfolder). If absent, we put it in the same folder as the --output_vcf folder (to be extracted from the it).
--output_folder no longer exists.
Currently the
--output_vcfparameter can only be the name of the file and not the full path (see https://github.com/IARCbioinfo/needlestack/blob/v1.1b/needlestack.nf#L505 and https://groups.google.com/forum/#!topic/nextflow/ctLboXGPdwI), and the path can be given using--output_folder.The rational was that the output also includes a
PDFfolder. However this can be confusing as putting the path inoutput_vcfis tempting. I propose to change the behaviour as follow:--output_vcf: is the path to the output vcf (e.g.my_vcf.vcfor/path/to/my_vcf.vfor../my_vcf.vcf)--output_pdf: is optional and is the folder where to store thePDFfolder (e.g..or/path/to/outfolder). If absent, we put it in the same folder as the--output_vcffolder (to be extracted from the it).--output_folderno longer exists.Any objection or better idea?